SMTL ID : 6eed.1

X-ray crystal structure of Pf-M1 in complex with inhibitor (6p) and catalytic zinc ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.301, H.305, E.324 Ligands: J6A.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.301, A:H.305, A:E.324, A:E.324, J6A.2

1 x J6A: (2R)-2-[(cyclohexylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide(Non-covalent)

J6A.2: 21 residues within 4Å: Chain A: T.110, Q.122, E.124, A.125, N.263, V.264, G.265, A.266, E.268, H.301, E.302, H.305, E.324, E.377, Y.380, T.381, T.382, Y.385, M.839 Ligands: ZN.1, PO4.15 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:Y.380, A:Y.385, A:Y.385, A:Y.385 Hydrogen bonds: A:G.265, A:A.266, A:Y.385, A:Y.385 Water bridges: A:A.266, A:A.266 pi-Stacking: A:Y.380 Halogen bonds: A:N.263, A:E.377

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: G.55 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.55, H2O.24, H2O.26, H2O.29, H2O.30, H2O.33 MG.4: 1 residues within 4Å: Chain A: E.762 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: D.243 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: N.888 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: V.342, D.563, S.564, A.566, R.569 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.569 Water bridges: A:D.563, A:S.564, A:A.566, A:R.569 GOL.8: 5 residues within 4Å: Chain A: H.458, K.481, Y.546, N.640, F.641 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.640 Water bridges: A:H.458, A:K.481, A:K.481, A:K.481, A:E.548 GOL.9: 6 residues within 4Å: Chain A: V.264, G.265, N.276, N.278, N.799, R.802 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.276, A:N.278, A:N.278, A:R.802 Water bridges: A:Q.843 GOL.10: 5 residues within 4Å: Chain A: V.157, H.199, Y.216, F.218, R.253 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.216, A:R.253, A:R.253 Water bridges: A:K.164, A:K.164, A:K.164, A:K.164, A:H.199 GOL.11: 4 residues within 4Å: Chain A: V.50, D.52, F.80, I.135 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.136, A:D.136 GOL.12: 6 residues within 4Å: Chain A: A.108, T.110, R.130, E.377, P.838, N.878 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.110, A:T.110 Water bridges: A:R.130, A:N.878 GOL.13: 10 residues within 4Å: Chain A: K.284, Y.685, F.686, H.691, V.692, D.693, Q.696, M.697, R.700, Y.730 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.284, A:Y.685, A:D.693, A:D.693, A:R.700, A:R.700 Water bridges: A:Q.696

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 4 residues within 4Å: Chain A: N.378, Y.380, T.381, T.842 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.380

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 6 residues within 4Å: Chain A: R.294, T.297, V.298, H.301, E.331 Ligands: J6A.2 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.294, A:R.294, A:E.331, A:E.331, A:E.331 Salt bridges: A:R.294, A:H.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinh, N.B. et al., Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. (2019)

Release Date

2018-12-26

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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